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First Large-Scale Proteogenomic Study of Breast Cancer Provides Insight into Potential Therapeutic Targets

News Release: May 25, 2016 — Building on data from The Cancer Genome Atlas (TCGA) project, a multi-institutional team of scientists has completed the first large-scale “proteogenomic” study of breast cancerlinking DNA mutations to protein signaling and helping pinpoint the genes that drive cancer. Conducted by members of the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC), including Baylor College of Medicine, Broad Institute of MIT and Harvard, Fred Hutchinson Cancer Research Center, New York University Langone Medical Center, and Washington University School of Medicine, the study takes aim at proteins, the workhorses of the cell, and their modifications to better understand cancer. Appearing in the Advance Online Publication of Nature on May 25, 2016, the study illustrates the power of integrating genomic and proteomic data to yield a more complete picture of cancer biology than either analysis could do alone.

The effort produced a broad overview of the landscape of the proteome (all the proteins found in a cell) and the phosphoproteome (the sites at which proteins are tagged by phosphorylation, a chemical modification that drives communication in the cell) across a set of 77 breast cancer tumors that had been genomically characterized in the TCGA project. Although the TCGA produced an extensive catalog of somatic mutations found in cancer, the effects of many of those mutations on cellular functions or patients’ outcomes are unknown. In addition, not all mutated genes are true “drivers” of cancer — some are merely “passenger” mutations that have little functional consequence. And some mutations are found within very large DNA regions that are deleted or present in extra copies, so winnowing the list of candidate genes by studying the activity of their protein products can help identify therapeutic targets.

“We don’t fully understand how complex cancer genomes translate into the driving biology that causes relapse and mortality,” said Matthew Ellis, director of the Lester and Sue Smith Breast Center at Baylor College of Medicine and a senior author of the paper. “These findings show that proteogenomic integration could one day prove to be a powerful clinical tool, allowing us to traverse the large knowledge gap between cancer genomics and clinical action.”

In this study, the researchers at the Broad Institute analyzed breast tumors using accurate mass, high-resolution mass spectrometry, a technology that extends the coverage of the proteome far beyond the coverage that can be achieved by traditional antibody-based methods. This allowed them to scale their efforts and quantify more than 12,000 proteins and 33,000 phosphosites, an extremely deep level of coverage.

“Advances in sample handling and instrumentation have brought on a revolution in mass-spectrometry-based proteomics,” said Steven Carr, director of the Broad Institute’s Proteomics Platform and a senior author of the study. “We can now apply that to the phosphoproteome, which is of central importance to understanding signaling in cancer and other diseases. Our approach produces robust and reproducible data, at a scale unachievable before.”

As with other cancers, breast cancer tumors are known to harbor many mutations, so studying them all would require an endless number of experiments to discern the effects of various combinations of mutations in a model system. With this approach, however, the team can study the cancer cell in which those mutations evolved and analyze the integrated output of the cell’s proteins.

"There is great potential for new insights to come from the combined analysis of cancer proteomic and genomic data, as proteomic data can now reproducibly provide information about protein levels and activities that are difficult or impossible to infer from genomic data alone,” said Douglas Lowy, acting director of the National Cancer Institute, National Institutes of Health.

This analysis uncovered new protein markers and signaling pathways for breast cancer subtypes and tumors carrying frequent mutations such as PIK3CA and TP53 mutations. The team also correlated copy number alterations (extra or missing DNA) in some genes with protein levels, allowing them to identify 10 new candidate regulators. Two of these candidate genes, SKP1 and CETN3, can be connected to the oncogene EGFR, which is a marker for a particularly aggressive breast cancer subtype, known as “basal-like” tumors.

Using transcriptional (mRNA) profiling, scientists have divided breast cancer into four major subtypes: luminal A and B subtypes, basal-like tumors, and HER2-enriched tumors. In this work, the researchers used proteomic and phosphoproteomic data to recapitulate basal and luminal subtypes. They were also able to identify a stromal-enriched cluster and, by clustering tumors based on phosphorylation pathways, they highlighted a G-protein-coupled receptor subgroup not seen with mRNA approaches.

In the study and treatment of breast cancer, scientists and physicians hope to identify more druggable kinase proteins in addition to HER2, which can be targeted with trastuzumab (Herceptin) but only in 20 percent of breast cancers that overexpress the HER2 protein. In this study, the researchers conducted an outlier analysis of the phosphorylation states of kinase enzymes, which highlighted aberrantly activated kinases in breast cancer samples, such as HER2, CDK12, PAK1, PTK2, RIPK2, and TLK2.

“It’s always been important to get through to the molecules at work in the cell — the proteins — and this integrative exercise really gives us a whole new understanding of the landscape,” said Li Ding, assistant director of the McDonnell Genome Institute at Washington University in St. Louis. “The proteogenomic approach shows potential for funneling down to a much smaller set of proteins and modifications that are the interesting drivers that we should think about from a therapeutic standpoint.”

The breast cancer team was co-led by Carr, Ellis, and Amanda Paulovich (Fred Hutchinson Cancer Research Center). Other researchers heavily involved in the work include co-first authors Philipp Mertins (Broad Institute), D.R. Mani (Broad Institute), Kelly Ruggles (NYU Langone Medical Center), and Michael Gillette (Broad Institute), in addition to co-authors David Fenyo (NYU Langone Medical Center), Karl Clauser (Broad Institute), Jana Qiao (Broad Institute), Charles Perou (University of North Carolina at Chapel Hill), Pei Wang (Icahn School of Medicine at Mount Sinai), Song Cao (Washington University in St. Louis), Sherri Davies (Washington University in St. Louis), and R. Reid Townsend (Washington University in St. Louis).

Paper cited: Proteogenomics connects somatic mutations to signaling in breast cancer. Nature. Advance Online Publication, May 25, 2016. DOI: 10.1038/nature18003.

About National Cancer Institute’s CPTAC
The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis technologies (proteogenomics) to different cancer types. CPTAC is composed of expertise in proteomics, genomics, cancer biology, oncology and clinical chemistry, while creating open community resources that are widely used by the cancer community. For further information about CPTAC, go to

About Baylor College of Medicine
Baylor College of Medicine ( in Houston is recognized as a premier academic health sciences center and is known for excellence in education, research and patient care. It is the only private medical school in the greater southwest and is ranked 20th among medical schools for research and 9th for primary care by U.S. News & World Report. Baylor is listed 20th among all U.S. medical schools for National Institutes of Health funding and No. 1 in Texas. Located in the Texas Medical Center, Baylor has affiliations with seven teaching hospitals and jointly owns and operates Baylor St. Luke’s Medical Center, part of CHI St. Luke’s Health. Currently, Baylor trains more than 3,000 medical, graduate, nurse anesthesia, physician assistant and orthotics students, as well as residents and post-doctoral fellows. For more information, visit and follow Baylor College of Medicine on Facebook ( and Twitter (

About the Broad Institute of MIT and Harvard
The Eli and Edythe L. Broad Institute of MIT and Harvard was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods, and data openly to the entire scientific community.

Founded by MIT, Harvard, and its affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff, and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to

About Fred Hutchinson Cancer Research Center
At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transplantation led to the development of immunotherapy, which harnesses the power of the immune system to treat cancer with minimal side effects. An independent, nonprofit research institute based in Seattle, Fred Hutch houses the nation’s first and largest cancer prevention research program, as well as the clinical coordinating center of the Women’s Health Initiative and the international headquarters of the HIV Vaccine Trials Network. Private contributions are essential for enabling Fred Hutch scientists to explore novel research opportunities that lead to important medical breakthroughs. For more information, visit or follow Fred Hutch on Facebook, Twitter or YouTube.

About New York University Langone Medical Center
NYU Langone Medical Center, a world-class, patient-centered, integrated academic medical center, is one of the nation’s premier centers for excellence in clinical care, biomedical research, and medical education. Located in the heart of Manhattan, NYU Langone is composed of four hospitals—Tisch Hospital, its flagship acute care facility; Rusk Rehabilitation; the Hospital for Joint Diseases, the Medical Center’s dedicated inpatient orthopedic hospital; and Hassenfeld Children’s Hospital, a comprehensive pediatric hospital supporting a full array of children’s health services across the Medical Center—plus the NYU School of Medicine, which since 1841 has trained thousands of physicians and scientists who have helped to shape the course of medical history. The Medical Center’s tri-fold mission to serve, teach, and discover is achieved 365 days a year through the seamless integration of a culture devoted to excellence in patient care, education, and research. For more information, go to, and interact with us on Facebook, Twitter, and YouTube.

About University of North Carolina Lineberger Comprehensive Cancer Center
One of only 45 NCI-designated comprehensive cancer centers, the University of North Carolina Lineberger Comprehensive Cancer Center brings together some of the most exceptional physicians and scientists in the country to investigate and improve the prevention, early detection and treatment of cancer. With research that spans the spectrum from the laboratory to the bedside to the community, UNC Lineberger faculty work to understand the causes of cancer at the genetic and environmental levels, to conduct groundbreaking laboratory research, and to translate findings into pioneering and innovative clinical trials. For more information, please visit

About Washington University School of Medicine in St. Louis
Washington University School of Medicine's 2,100 employed and volunteer faculty physicians also are the medical staff of Barnes-Jewish and St. Louis Children's hospitals. The School of Medicine is one of the leading medical research, teaching and patient-care institutions in the nation, currently ranked sixth in the nation by U.S. News & World Report. Through its affiliations with Barnes-Jewish and St. Louis Children's hospitals, the School of Medicine is linked to BJC HealthCare. The university’s McDonnell Genome Institute is a world leader in the fast-paced, constantly changing field of genomics. The institute pushes the limits of academic research by creating, testing, and implementing new approaches to the study of biology with the goal of understanding human health and disease, as well as evolution and the biology of organisms. For more information, go to